Molecular biology and genetics are currently at the center of an information revolution. High-throughput techniques generate very large amounts of heterogeneous data. There is a large gap between our ability to collect data and our ability to interpret it. The challenge faced by today's researchers is to develop effective ways to analyze the vast amount of data that has been and will continue to be collected. First released in 2001, Onto-Tools is an open access software suite that partially addresses this problem. This is achieved by using a probabilistic functional analysis that bridges the gap between low-level, high-throughput gene expression data and high-level functional knowledge. This proposal further addresses the existing computational challenge by developing novel data analysis techniques based on latent semantic indexing and statistical analysis. These techniques will be able to discover previously unknown interactions and phenomena at the genetic level. New gene-to-gene interactions, novel gene-to-function assignments, and perturbed interactions between biological processes can be discovered using this approach. Most techniques that try to predict gene functions rely on genes with known function and use sequence similarity, 3D structure similarity, or both, to extrapolate the functionality of novel genes. Our approach is innovative because it uses real expression data to extract the functions of the target genes. The proposed tool, Onto-Analyzer, will offer these capabilities as part of the Onto-Tools suite. Onto-Tools will also be enhanced by adding support for 17 new organisms. The goal of developing advanced computational tools is also obstructed by another gap in the current knowledge. Successful public bioinformatics software has a large and demanding user community. To radically evolve software and, at the same time, to maintain the expected level of service usually requires large resources, unavailable to small research groups. Therefore migration to open source platform is desirable. In order to enable this migration, the evolvability, reparability, modifiability, portability, understandability, and the documentation of Onto-Tools will be improved. The proposed research will develop a set of software evolution tools to address these issues trough software, visualization, change impact analysis, traceability link recovery, and re-documentation. The enhanced Onto-Tools will continue to be freely available. Onto-Analyzer and the software evolution tools developed under this proposal will be made freely available to the research community, as well.